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Epidemiology and evolution of fungal foliar pathogens in the face of changes in crop fertilization : application of evolutionary-ecological theory to crop epidemiology

Abstract : The quest for a sustainable agriculture requires a reduction in the use of synthetic inputs. In this perspective, agroecology seeks to use interactions between organisms in the agroecosystem to replace inputs by ecosystem services, such as the natural regulation of pests and diseases. In this context, this thesis studies the effect of crop fertilization on epidemics of crop fungal foliar pathogens. We also take into account the evolution of these pathogens in response to fertilization scenarios. This allows us to study the sustainability of agricultural practices that contribute to the regulation of epidemics. To answer these questions, we adopted a modelling approach that simulates the effect of different fertilization scenarios. The starting point and originality of our approach was to consider the pathosystem as a consumer-resource system and to use concepts of evolutionary ecology to answer the abovementioned agronomic questions. In the two models developed in this thesis, fertilization directly determines the quantity of resources available for the pathogen. We focus on one of the pathogen's life history traits, the latent period (time period between infection and the onset of sporulating lesions), which corresponds to the minimum duration of an infectious cycle and constrains the pathogen's resource allocation strategy. The latent period determines the amount of resource that will be allocated to either growth of mycelium (and therefore to pathogen size at maturity) or to sporulation (proportional to the pathogen’s size). The models we developed make it possible to study the epidemiological and evolutionary responses of fungal foliar pathogens to crop fertilization. We parameterized our models according to our biological knowledge of the wheat-rust pathosystem. Our modelling work encompasses different spatial and temporal scales: from the lesion where the pathogen feeds directly on its host, to the field and the landscape where the spores that flow between fields are the source of epidemics in the agroecosystem. The first model, at the intersection of the "SEIR" epidemiological models and structured population models, covers the scales of a lesion, the crop canopy and the field. The second model, at the intersection of SEIR and spatial landscape epidemiology models, covers the scales of the field and the agricultural landscape. We study epidemiological and evolutionary dynamics of pathogen populations by comparing empirical and invasion fitness concepts. We show that crop fertilization, by determining the dynamics of available resources for pathogens, has a strong impact on foliar fungal epidemics. Our models predict that pathogen latent period evolves in response to various ecological trade-offs; on the one hand to optimize resources allocation at the leaf scale, on the other hand to win the race against canopy growth. By changing the leaf metabolite content and the rate of canopy growth, fertilization therefore impacts both epidemics and evolutionary responses of pathogen latent period. At the landscape scale, the introduction of various fertilization practices in a previously homogeneous landscape could help to partially regulate epidemics. However, our model predicts that the beneficial effects of heterogeneity will vanish due to the evolution and diversification of pathogens in heterogeneous landscapes. This work sets the stage for further work on the effect and sustainability of agricultural practices on the regulation of crop epidemics in agroecosystems. Finally, by performing a meta-analysis, we bring out a strong relation between pathogen trophic type and latent period, suggesting that different trophic types of pathogens will respond differently to decreasing fertilization scenarios
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Submitted on : Friday, October 25, 2019 - 2:09:08 PM
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  • HAL Id : tel-02333571, version 1

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Pierre-Antoine Précigout. Epidemiology and evolution of fungal foliar pathogens in the face of changes in crop fertilization : application of evolutionary-ecological theory to crop epidemiology. Other [q-bio.OT]. Université Sorbonne Paris Cité, 2018. English. ⟨NNT : 2018USPCC108⟩. ⟨tel-02333571⟩

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